There are 4 metacolumns and 6 metarows in the
top half and this is duplicated again in the bottom half. Therefore, if you
wanted to grid every spot no this microarray, there would be a total of 48
grids each composed of 24 x 23 arrays of spots.

The experiment was designed to duplicate the
DeRisi diauxic shift paper (1997). All of the RNA was prepared by Dr. Laura
Hoopes' lab from two populations of cells. One group of cells was harvested
at an optical density of 0.6 and the other was harvested at an optical density
of 4.0. RNA was isolated and cDNA generated using one of three methods (indirect,
direct, or 3DNA). Our goal was not to rate the three methods, but to determine
if they worked and what pros/cons each method has. All methods did produce
strong signals, so we are comfortable with GCAT members using the one they
like best. It may be equipment, number of steps, time constraints, costs,
etc. But GCAT does not want to tell people which method to do. We just want
to make each method possible and to maximize your success.

The "Indirect Dye"method uses amino
allyl dUTP to label the cDNA. This method prevents the dyes from creating
a bias in the cDNA synthesis. The "Direct Dye" method uses Cy3/Cy5-coupled
dUTP for cDNA synthesis. This reduces the number of steps to make the labeled
cDNA. The 3DNA method uses Genisphere's dendrimer with about 200 dyes per
cDNA so the signal is very strong. You can download the methods we used, and
personal comments from the table below: